added documentation

doc/src/pair_mesocnt.txt

@@ -0,0 +1,132 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+pair_style mesocnt command :h3
+
+[Syntax:]
+
+pair_style mesocnt :pre
+
+[Examples:]
+
+pair_style mesocnt
+pair_coeff * * 10_10.cnt :pre
+
+[Description:]
+
+Style {mesocnt} implements a mesoscopic potential
+for the interaction of carbon nanotubes (CNTs). In this potential,
+CNTs are modelled as chains of cylindrical segments in which
+each infinitesimal surface element interacts with all other
+CNT surface elements with the Lennard-Jones (LJ) term adopted from
+the "airebo"_pair_airebo.html style. The interation energy
+is then computed by integrating over the surfaces of all interacting
+CNTs.
+
+The potential is based on interactions between one cylindrical
+segment and infinitely or semi-infinitely long CNTs as described
+in "(Volkov1)"_#Volkov1. Chains of segments are
+converted to these (semi-)infinite CNTs bases on an approximate
+chain approach outlined in "(Volkov2)"_#Volkov2.
+This allows to simplify the computation of the interactions
+significantly and reduces the computational times to the
+same order of magnitude as for regular bead spring models
+where beads interact with the standard "pair_lj/cut"_pair_lj.html
+potential.
+
+In LAMMPS, cylindrical segments are represented by bonds. Each
+segment is defined by its two end points ("nodes") which correspond
+to atoms in LAMMPS. For the exact functional form of the potential
+and implementation details, the reader is referred to the 
+original papers "(Volkov1)"_#Volkov1 and 
+"(Volkov2)"_#Volkov2.
+
+The potential requires tabulated data provided in a single ASCII 
+text file specified in the "pair_coeff"_pair_coeff.html command. 
+The first line of the file provides a time stamp and
+general information. The second line lists four integers giving
+the number of data points provided in the subsequent four
+data tables. The third line lists four floating point numbers: 
+the CNT radius R, the LJ parameter sigma and two numerical 
+parameters delta1 and delta2. These four parameters are given
+in Angstroms. This is followed by four data tables each separated
+by a single empty line. The first two tables have two columns
+and list the parameters uInfParallel and Gamma respectively.
+The last two tables have three columns giving data on a quadratic
+array and list the parameters Phi and uSemiParallel respectively.
+uInfParallel and uSemiParallel are given in eV/Angstrom, Phi is
+given in eV and Gamma is unitless.
+
+Potential files for CNTs can be readily generated using the freely 
+available code provided on
+
+https://github.com/phankl/cntpot
+
+Using the same approach, it should also be possible to
+generate potential files for other 1D systems such as
+boron nitride nanotubes.
+
+NOTE: LAMMPS comes with one {mesocnt} style potential file
+where the default number of data points per table is 1001.
+This is sufficient for NVT simulations. For proper energy
+conservation, we recommend using a potential file where
+the resolution for Phi is at least 2001 data points.
+
+NOTE: The {mesocnt} style requires CNTs to be represented
+as a chain of atoms connected by bonds. Atoms need
+to be numbered consecutively within one chain. 
+Atoms belonging to different CNTs need to be assigned
+different molecule IDs.
+
+A full summary of the method and LAMMPS implementation details
+are expected to soon become available in Computer Physics
+Communications.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This pair style does not support mixing.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+The mesocnt pair style do not write their information to "binary restart
+files"_restart.html, since it is stored in tabulated potential files.
+Thus, you need to re-specify the pair_style and pair_coeff commands in
+an input script that reads a restart file.
+
+These pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command.  They do not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+The mesocnt style is part of the USER-MESOCNT package. It is only
+enabled if LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+This pair potential requires the "newton"_newton.html setting to be
+"on" for pair interactions.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
+:link(Volkov1)
+[(Volkov1)] Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010).
+
+:link(Volkov2)
+[(Volkov2)] Volkov, Simov and Zhigilei, APS Meeting Abstracts, 
+Q31.013 (2008).

doc/src/pairs.txt

@@ -72,6 +72,7 @@ Pair Styles :h1
    pair_meam_spline
    pair_meam_sw_spline
    pair_meso
+   pair_mesocnt
    pair_mgpt
    pair_mie
    pair_mm3_switch3_coulgauss

src/USER-MESOCNT/pair_mesocnt.cpp

@@ -13,6 +13,7 @@
 
 /* ----------------------------------------------------------------------
    Contributing author: Philipp Kloza (University of Cambridge)
+                        pak37@cam.ac.uk
 ------------------------------------------------------------------------- */
 
 #include <cmath>